rs4078417

Variant names:

• chr14-51290164-A-C
• rs4078417
• XR_007064164.1:n.633+2101A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064164.1(LOC124903315):​n.633+2101A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,164 control chromosomes in the GnomAD database, including 6,356 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (6356 hom., cov: 32)
• Consequence: LOC124903315 XR_007064164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.774
• Publications: 3 publications found

Genes affected

LOC124903315 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38530 AN: 152046 Hom.: 6352 Cov.: 32

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.257

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.253 AC: 38540 AN: 152164 Hom.: 6356 Cov.: 32 AF XY: 0.251 AC XY: 18694 AN XY: 74384

African (AFR) AF: 0.0640 AC: 2659 AN: 41550

American (AMR) AF: 0.327 AC: 5003 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3470

East Asian (EAS) AF: 0.0402 AC: 208 AN: 5178

South Asian (SAS) AF: 0.223 AC: 1077 AN: 4822

European-Finnish (FIN) AF: 0.316 AC: 3344 AN: 10574

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24282 AN: 67974

Other (OTH) AF: 0.254 AC: 536 AN: 2114

Alfa AF: 0.315 Hom.: 16419

Bravo AF: 0.248

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.45
PhyloP100		0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4078417; hg19: chr14-51756882;